Genetics: Analysis and Principles 5th Edition by Robert Brooker

Exercise 8

In the following drawing, the top strand is the template DNA, and the bottom strand shows the lagging strand prior to the action of DNA polymerase I. The lagging strand contains three Okazaki fragments. The RNA primers have not yet been removed.The top strand is the template DNA.
a. Which Okazaki fragment was made first, the one on the left or the one on the right
B. Which RNA primer would be the first one to be removed by DNA polymerase I, the primer on the left or the primer on the right For this primer to be removed by DNA polymerase I and for the gap to be filled in, is it necessary for the Okazaki fragment in the middle to have already been synthesized Explain
c. Let's consider how DNA ligase connects the left Okazaki fragment with the middle Okazaki fragment. After DNA polymerase I removes the middle RNA primer and fills in the gap with DNA, where does DNA ligase function See the arrows on either side of the middle RNA primer. Is ligase needed at the left arrow, at the right arrow, or both
D. When connecting two Okazaki fragments, DNA ligase uses NAD + or ATP as a source of energy to catalyze this reaction. Explain why DNA ligase needs another source of energy to connect two nucleotides, but DNA polymerase needs nothing more than the incoming nucleotide and the existing DNA strand. Note: You may want to refer to Figure 11.16 to answer this question.FIGURE 11.16 The enzymatic action of DNA polymerase. An incoming deoxyribonucleoside triphosphate (dNTP) is cleaved to form a nucleoside monophosphate and pyrophosphate (PP i ). The energy released from this exergonic reaction allows the nucleoside monophosphate to form a covalent bond at the 3 end of the growing strand. This reaction is catalyzed by DNA polymerase. PP i is released.